AFM-Based Nanoscratching: A 3D Molecular Dynamics Simulation With Experimental Verification

2014 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Gold Substrate ◽  
Three Dimensional Model ◽  
Friction Forces ◽  
Defect Mechanism

In this paper, a developed three-dimensional model for AFM-based nanomachining is applied to study mechanical scratching at the nanoscale. The correlation between the scratching conditions, including applied force, scratching depth, and distant between any two scratched grooves, and the defect mechanism in the substrate/workpiece is investigated. The simulations of nanoscratching process are performed on different crystal orientations of single-crystal gold substrate, Au(100), Au(110), and Au(111). The material deformation and groove geometry are extracted from the final locations of atoms, which are displaced by the rigid indenter. The simulation also allows for the prediction of normal and friction forces at the interface between the indenter and substrate. An AFM is used to conduct actual scratching at the nanoscale, and provide measurements to which the MD simulation predictions are compared. The predicted forces obtained from MD simulation compares qualitatively with the experimental results.

Three-dimensional model and molecular dynamics simulation of the active site of the self-splicing intervening sequence of the bacteriophage T4 nrdB messenger RNA

Biochemistry ◽  
1990 ◽  
Vol 29 (45) ◽  
pp. 10317-10322 ◽  
Author(s):  
Lennart Nilsson ◽  
Agneta Aahgren-Staalhandske ◽  
Ann Sofie Sjoegren ◽  
Solveig Hahne ◽  
Britt Marie Sjoeberg
Keyword(s):  
Molecular Dynamics ◽  
Active Site ◽  
Messenger Rna ◽  
Bacteriophage T4 ◽  
Three Dimensional ◽  
The Self ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Self Splicing

Effects of Adhesion and Friction on the Pattern Transfer in Nanoimprint Lithography: A Molecular Dynamics Simulation

2005 ◽  
Author(s):  
Ji-Hoon Kang ◽  
Kwang-Seop Kim ◽  
Kyung-Woong Kim
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Polymer Film ◽  
Nanoimprint Lithography ◽  
Direct Contact ◽  
Md Simulation ◽  
Dynamics Simulation ◽  
Pattern Transfer ◽  
Friction Forces ◽  
Simulation Results

Due to the direct contact between the stamp and polymer film during the nanoimprint lithography (NIL) process, the adhesion and friction are unavoidable. To investigate the effect of adhesion and friction on the pattern transfer, molecular dynamics (MD) simulation of NIL is performed. As the simulation results, the adhesion and friction forces between the stamp and polymer film are calculated and the effects of the adhesion and friction on the pattern transfer are studied.

A Study on Surface Friction on Gold Substrate With 2D Molecular Dynamics Simulation

2008 ◽  
Author(s):  
Hualong Yu ◽  
Q. Jane Wang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Md Simulation ◽  
Surface Friction ◽  
Gold Surface ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Two Dimensional ◽  
Gold Substrate ◽  
Simulation Results

This paper reports a study on the contact and friction between a gold surface and a rigid tip with a two-dimensional (2D) classical Molecular Dynamics (MD) simulation method. A multiscale method is used in the MD simulation. The MD simulation results are compared with the Hertzian cylindrical contact results. A criterion for the transition from surface sliding to surface scratching is also discussed with the assistance of stress analyses.

Nanoindentation Models With Realistic AFM Tip Geometries

2015 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan
Keyword(s):  
Molecular Dynamics ◽  
Atomic Force Microscopy ◽  
Md Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Gold Substrate ◽  
Force Microscopy ◽  
Atomic Force ◽  
Defect Mechanism ◽  
Tip Radius

In this paper, a three-dimensional computational model for Atomic Force Microscopy (AFM) based nanoindentation processes is being developed. Molecular Dynamics (MD) and Finite Element (FE) techniques are used to model and simulate mechanical indentation at the nanoscale. The correlation between the indentation conditions, including applied force and tip radius, and defect mechanism in substrate is investigated. The tip geometries used in the model are the same as those used in the experiments. The MD simulations of nanoindentation process are performed on different crystal orientations of single-crystal gold substrate, Au(100), Au(110), and Au(111). In MD simulation, the material deformation is extracted from the final locations of atoms, which are displaced by the rigid indenter. The simulation also allows for the prediction of forces at the interface between the indenter and substrate. In addition to the modeling, an AFM is used to conduct actual indentation at the nanoscale, and provide measurements to which the simulation predictions are compared.

scholarly journals Influence of Nanoscale Textured Surfaces and Subsurface Defects on Friction Behaviors by Molecular Dynamics Simulation

Nanomaterials ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 1617 ◽  
Author(s):  
Ruiting Tong ◽  
Zefen Quan ◽  
Yangdong Zhao ◽  
Bin Han ◽  
Geng Liu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Friction Force ◽  
Copper Substrate ◽  
Dynamics Simulation ◽  
Textured Surfaces ◽  
Friction Forces ◽  
Subsurface Structures ◽  
Texture Orientation ◽  
Subsurface Defects

In nanomaterials, the surface or the subsurface structures influence the friction behaviors greatly. In this work, nanoscale friction behaviors between a rigid cylinder tip and a single crystal copper substrate are studied by molecular dynamics simulation. Nanoscale textured surfaces are modeled on the surface of the substrate to represent the surface structures, and the spacings between textures are seen as defects on the surface. Nano-defects are prepared at the subsurface of the substrate. The effects of depth, orientation, width and shape of textured surfaces on the average friction forces are investigated, and the influence of subsurface defects in the substrate is also studied. Compared with the smooth surface, textured surfaces can improve friction behaviors effectively. The textured surfaces with a greater depth or smaller width lead to lower friction forces. The surface with 45° texture orientation produces the lowest average friction force among all the orientations. The influence of the shape is slight, and the v-shape shows a lower average friction force. Besides, the subsurface defects in the substrate make the sliding process unstable and the influence of subsurface defects on friction forces is sensitive to their positions.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

Dynamic Simulation Analysis of the Crane Hoisting Process Based on Adams

2014 ◽  
Vol 940 ◽  
pp. 132-135 ◽  
Author(s):  
Yi Fan Zhao ◽  
Ling Sha ◽  
Yi Zhu
Keyword(s):  
Dynamic Simulation ◽  
Simulation Analysis ◽  
Three Dimensional ◽  
Wire Rope ◽  
Dynamics Simulation ◽  
Dimensional Model ◽  
Analysis Model ◽  
Three Dimensional Model ◽  
Adams Software ◽  
Simulation Results

Established the dynamics simulation analysis model of crane hoisting mechanism based on the theory of dynamics in Adams software, and then through the three dimensional model of lifting mechanism dynamics entities, the constraints, load, drive can be added, the motion law can be defined to simulation analysis the change of the force of wire rope, the change of displacement, velocity and acceleration of lifting weight in the lifting process. On the basis of the simulation results, it can make a great improvement for the structure of crane and provide a meaningful theoretical reference for the hoisting machinery innovation design.

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

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